We numerically verify better fluid mixing efficiency can be achieved by alternating injection scheme in a heterogeneous porous medium, whose permeability heterogeneity is characterized by two statistical parameters, i.e., the variance s and the correlation length l. Nevertheless, the fingering pattern is strongly affected by permeability distribution to result in similar fingering interface on each of injected layer of less viscous fluids. Instead of randomly chaotic fingering interaction in a homogeneous condition, more orderly channeling interaction occurs in a heterogeneous medium. As a result, higher Peclet number Pe (relative measure of advection and diffusion effects) generally leads to worse mixing efficiency in a heterogeneous medium, which might contradict the result found in a homogeneous case. By the same token, in the cases which strong chaotic fingering interaction already exists in homogeneous conditions, e.g., sufficiently short alternating injection interval Δt, large viscosity contrast A and high Pe, the presence of permeability heterogeneity would constrain the randomly chaotic fingering interaction and favors the more orderly channeling interaction, so that mixing efficiency is deteriorated compared with the corresponding homogeneous case.